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Learn antimicrobial susceptibility testing techniques and how whole-genome sequencing and bioinformatics can be used to understand AMR
Antimicrobial resistance (AMR) is a global public health emergency and threatens the safe delivery of modern medical care. A recent study estimated that there were 4.95 million deaths associated with AMR bacterial infections in 2019. Global projections of the negative impact of AMR predict the loss of nearly 10 million lives per year, and a cumulative loss of global production up to 100 trillion US dollars by 2050. AMR requires immediate, concerted, international, collaborative action to monitor its prevalence and spread throughout the world.
The importance of this has been recognised both by the United Nations, and by the World Health Organisation; the latter has published a list of priority pathogens and a global strategy for AMR surveillance.
In collaboration with the National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Services, Johannesburg, South Africa, we are pleased to announce our 2026 global training course in AMR of bacterial pathogens in Africa. This course aims to address regionally specific AMR-associated challenges through knowledge transfer and skills development by global experts.
This week-long course will include an introduction to AMR with hands-on laboratory practicals for AMR detection through molecular and phenotypic testing accompanied by theoretical training on the evolution and spread of AMR and utilisation of whole-genome sequencing and bioinformatics analysis methods for AMR surveillance and control.
It will also provide an opportunity for participants to network and potentially build a regional AMR community to support long-term partnerships and collaborations.
This course is open to applicants based in Africa only, who are actively engaged in, or soon to commence related research or work. This may include diagnostic stewardship, antimicrobial stewardship, infection prevention and control, or generate policies related to AMR in bacteria. Applicants should be PhD students, clinical trainees, or specialists in medical microbiology or bioinformatics, postdoctoral scientists, senior technicians, or research assistants with a Master’s degree.
After completing this course, you will be able to:
- Carry out standard laboratory methods for antimicrobial susceptibility testing (e.g. disk testing and MIC determination)
- Describe the principles and practice of quality assurance and control in AMR surveillance techniques, antimicrobial susceptibility testing and reporting.
- Discuss the range of control strategies for AMR in human and veterinary medicine (e.g. antimicrobial stewardship, infection control and policies).
- Use appropriate software tools to analyse WGS data for assembly of bacterial genomes, detect resistant variants and conduct phylogenetic analysis.
- Analyse and interpret genomics data for AMR surveillance.
The course will consist of a series of lectures and hands-on laboratory and computational practicals. Participants will learn standard international methods for the detection of antimicrobial resistance in bacteria. They will also complete computational practicals covering the investigation, tracking and understanding AMR in bacteria.
Topics will include:
- Epidemiology of AMR pathogens and national surveillance programmes
- Clinical importance of AMR
- Causes and biological mechanisms of resistance in Gram-positive and Gram-negative bacteria
- Antimicrobial susceptibility testing (AST) methods e.g. disc testing, automated systems, minimum inhibitory concentration (MIC), breakpoints and reporting, QC/QA
- Antibiotic policies and stewardship
- Tackling AMR using a One Health Approach
- Whole genome sequencing (WGS)
- Web-based and command line tools for pathogen genomics analysis
- Genomic surveillance of AMR
Course Instructors
- Beth Blane, University of Cambridge, UK
- Ewan Harrison, Wellcome Sanger Institute, UK
- Vindana Chibabhai, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases (NICD), South Africa
- Francesc Coll I Cerezo, Instituto de Biomedicina de Valencia
- Fahad Khokhar, University of Cambridge
- Collins Kigen, Kenya Medical Research Institute(KEMRI)/WRAIR-Africa MicroHub Lab, Kenya
- Cebile Lekhuleni, National Institute for Communicable Diseases (NICD), South Africa
- Caroline Maluleka, Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), National Institute for Communicable Diseases (NICD), South Africa
- Fahima Moosa, National Institute for Communicable Diseases (NICD), South Africa
- Anthony Smith, National Institute for Communicable Diseases (NICD), South Africa
- Augusto Messa Junior, Centro de Investigação em Saúde de Manhiça, Mozambique
- Stanford Kwenda, African Society of Medical Laboratory Sciences, South Africa
- Tsidiso Maphanga, National Institute for Communicable Diseases (NICD), South Africa
- Ruth Mogokotleng, National Institute for Communicable Diseases (NICD), South Africa
- Silondiwe Nzimande, National Institute for Communicable Diseases (NICD), South Africa
- Miriam Mwamba, National Institute for Communicable Diseases (NICD), South Africa
Wellcome Connecting Science Team
- Martin Aslett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
- Cassandra Soo, Laboratory Courses Manager
- Aaron Dean, Laboratory Technical Officer
- Christopher Adamson, Laboratory Operations Officer
- Isabela Malta, Assistant Overseas Courses Manager
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
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